Mercurial > repos > mingchen0919 > mygene_and_myvariant
changeset 2:a00a424ff951 draft
add r-httr package
| author | mingchen0919 |
|---|---|
| date | Tue, 20 Mar 2018 23:19:14 -0400 |
| parents | f8ac93c41720 |
| children | 5bfde1050a60 |
| files | variant_simple_search.Rmd variant_simple_search.xml variant_simple_search_render.R |
| diffstat | 3 files changed, 24 insertions(+), 13 deletions(-) [+] |
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--- a/variant_simple_search.Rmd Tue Mar 20 13:59:04 2018 -0400 +++ b/variant_simple_search.Rmd Tue Mar 20 23:19:14 2018 -0400 @@ -1,12 +1,9 @@ --- -title: 'HTML report title' +title: 'myvariant.info: simple search' output: html_document: - number_sections: true - toc: true theme: cosmo highlight: tango - code_folding: hide --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} @@ -23,5 +20,19 @@ opt ``` +```{r} +req = POST('http://myvariant.info/v1/variant?', + add_headers( + 'accept' = "application/json", + 'Content-Type' = "application/x-www-form-urlencoded" + ), + body = list(ids = opt$X_q, dotfield = 'true'), encode = 'form') +json = content(req, as = 'text') +df = t(as.data.frame(fromJSON(json))) +colnames(df) = strsplit(ids, ',')[[1]] +datatable(df) +``` + +
--- a/variant_simple_search.xml Tue Mar 20 13:59:04 2018 -0400 +++ b/variant_simple_search.xml Tue Mar 20 23:19:14 2018 -0400 @@ -10,6 +10,7 @@ <requirement type="package" version="0.2">r-dt</requirement> <requirement type="package" version="3.1">r-curl</requirement> <requirement type="package" version="1.95_4.8">r-rcurl</requirement> + <requirement type="package" version="1.3.1">r-httr</requirement> </requirements> <macros> <import>mygene_and_myvariant_macros.xml</import> @@ -23,11 +24,11 @@ Rscript '${__tool_directory__}/variant_simple_search_render.R' - -o $report - -d $report.files_path - -s $sink_message - -q $variant_query - -f $return_fields + -o '$report' + -d '$report.files_path' + -s '$sink_message' + -q '$variant_query' + -f '$return_fields' @@ -35,13 +36,11 @@ <inputs> <param type="text" name="variant_query" label="Search keywords" optional="False"> <sanitizer> - <valid initial="default"> - <add preset="string.printable"/> - </valid> + <valid initial="string.printable"/> </sanitizer> </param> <param type="select" name="return_fields" label="Returned fields" optional="False" multiple="True"> - <expand macro="fields" /> + <expand macro="fields"/> </param> </inputs> <outputs>